39,735 results match your criteria sequence typing


Following Transplantation for Acute Myelogenous Leukemia, Donor Better Protects against Relapse than .

J Immunol 2021 Jun 11. Epub 2021 Jun 11.

Department of Structural Biology, Stanford University, Stanford, CA;

In the treatment of acute myelogenous leukemia with allogeneic hematopoietic cell transplantation, we previously demonstrated that there is a greater protection from relapse of leukemia when the hematopoietic cell transplantation donor has either the / genotype or a genotype having two or more gene segments. In those earlier analyses, genotyping could only be assessed at the low resolution of gene presence or absence. To give the analysis greater depth, we developed high-resolution sequence-based typing that defines all the alleles and distinguishes the expressed alleles from those that are not expressed. Read More

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Chlamydia pecorum detection in aborted and stillborn lambs from Western Australia.

Vet Res 2021 Jun 11;52(1):84. Epub 2021 Jun 11.

Centre for Animal Production and Health, Murdoch University, South Street, Murdoch, WA, 6150, Australia.

Lamb survival is an important welfare and productivity issue for sheep industries worldwide. Lower lamb survival has been reported for primiparous ewes, but the causes of this are not well studied. The aim of this study was to determine causes of perinatal deaths for lambs born to primiparous ewes in Western Australia, and identify if infectious diseases are implicated. Read More

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Molecular characterization of decreased susceptibility to ceftriaxone and genotyping of Neisseria gonorrheae isolates in New Delhi, India.

Diagn Microbiol Infect Dis 2021 May 11;101(1):115423. Epub 2021 May 11.

Department of Dermatology & Venereology, All India Institute of Medical Sciences, New Delhi, India.

Data on genetic characteristics of Neisseria gonorrhoeae isolates exhibiting decreased susceptibility to extended-spectrum cephalosporins in India is deficient. In this study, we have sequenced penA, porB, mtrR and ponA and bla genes in 70 clinical isolates of NG with varying ceftriaxone MICs. Amongst these, 22 (31. Read More

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Successful Isavuconazole Salvage Therapy for a Cryptococcus deuterogattii (AFLP6/VGII) Disseminated Infection in a European Immunocompetent Patient.

Mycopathologia 2021 Jun 11. Epub 2021 Jun 11.

Medical Mycology Laboratory, Department of Plant Production and Microbiology, University Miguel Hernández, Campus of Sant Joan D'Alacant, 03550, Alicante, Spain.

Members of the Cryptococcus gattii species complex are notorious causes of cryptococcosis as they often cause severe, life-threatening infections. Here we describe a case of a severe disseminated C. deuterogattii infection in a previously healthy patient who was initially treated with amphotericin B, 5-fluorocytosine and fluconazole, which led to a good neurological response, but the infection in the lungs remained unaltered and was not completely resolved until switching the antifungal therapy to isavuconazole. Read More

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Phenotypic and genotypic characterization of mcr-1-positive multidrug-resistant Escherichia coli ST93, ST117, ST156, ST10, and ST744 isolated from poultry in Poland.

Braz J Microbiol 2021 Jun 10. Epub 2021 Jun 10.

The Faculty of Veterinary Medicine, Department of Epizootiology and Clinic of Birds and Exotic Animals, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland.

Background: A plasmid-mediated mechanism of bacterial resistance to polymyxin is a serious threat to public health worldwide. The present study aimed to determine the occurrence of plasmid-mediated colistin resistance genes and to conduct the molecular characterization of mcr-positive Escherichia coli strains isolated from Polish poultry.

Methods: In this study, 318 E. Read More

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Genetic diversity and phylogenetic analysis of the surface layer protein A gene (slpA) among Clostridioides difficile clinical isolates from Tehran, Iran.

Anaerobe 2021 Jun 7:102403. Epub 2021 Jun 7.

Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Clostridioides difficile is the most common causative agent of healthcare-associated diarrhea. C. difficile strains produce a crystalline surface layer protein (SlpA), encoded by the slpA gene. Read More

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Sink drains as reservoirs of VIM-2 metallo-β-lactamase-producing Pseudomonas aeruginosa in a Belgian intensive care unit: relation to patients investigated by whole genome sequencing.

J Hosp Infect 2021 Jun 7. Epub 2021 Jun 7.

Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.

Background: Hospital acquired infections caused by VIM encoded metallo-β-lactamase-positive Pseudomonas aeruginosa are a major problem in intensive care units (ICUs) worldwide. A previous study conducted in the UZ Brussel hospital revealed that sink drains of the ICU were a possible source of various multi-drug resistant pathogenic bacteria.

Aim: We aimed to investigate the presence and persistence of VIM P. Read More

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Culture-independent genotyping revealed three strain clusters in a potential Neisseria gonorrhoeae outbreak in young heterosexuals (<25), the Netherlands, October 2017 to March 2019.

Sex Transm Dis 2021 Jan 12. Epub 2021 Jan 12.

1 Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ Maastricht, the Netherlands 2 Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, PO Box 33, 6400 AA Heerlen, the Netherlands 3 Department of Health Promotion, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ Maastricht, the Netherlands.

Background: Investigation was undertaken to determine the genetic relatedness of Neisseria gonorrhoeae (NG) isolates of young (<25) heterosexuals of a potential outbreak from October 2017 to March 2019 in South-Limburg, the Netherlands.

Methods: Data and residual sample material of routine diagnostics were retrieved for outbreak cases (78/81), young heterosexuals at baseline (January 2016 to September 2017, n=30), and men who have sex with men (MSM) (2018, n=47). Total DNA was isolated, and NG was genotyped using culture-free NG multi-antigen sequence typing. Read More

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January 2021

A comparison of Treponema pallidum subspecies pallidum molecular typing systems: multilocus sequence typing (MLST) vs enhanced CDC Typing (ECDCT).

Sex Transm Dis 2021 Mar 16. Epub 2021 Mar 16.

Department of Neurologya, University of Washington, Seattle, WA.

Background: At least three syphilis typing systems are proposed. Recent work suggests that multilocus sequence typing (MLST) may be superior to enhanced CDC typing (ECDCT) by yielding a higher discriminatory power. The goal of this study was to compare the two systems and identify associations between neurosyphilis and strain types. Read More

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Characterization of multidrug-resistant and virulent Klebsiella pneumoniae strains belonging to the high-risk clonal group 258 (CG258) isolated from inpatients in northeastern Brazil.

Arch Microbiol 2021 Jun 10. Epub 2021 Jun 10.

Postgraduate Program in Environmental Technology, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.

Multidrug-resistant (MDR) and hypervirulent Klebsiella pneumoniae (hvKp) clones have become a major threat to global public health. The clonal group 258 (CG258) is considered a high-risk CG and the K. pneumoniae strains belonging to it are often multi-resistant and to spread mainly in the hospital environment. Read More

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rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.

Microb Genom 2021 Jun;7(6)

The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, the Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda.

The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens (, , , , and species) using WGS data generated from Illumina's sequencing platforms. Read More

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sp. nov., isolated from rhizosphere soil of .

Int J Syst Evol Microbiol 2021 Jun;71(6)

Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.

A novel Gram-stain positive, facultatively anaerobic, motile, irregularly rod-shaped bacterium, designated GY 10621, was isolated from rhizosphere soil of in Beihai City, Guangxi Province, PR China, and characterized using a polyphasic taxonomic approach. GY 10621 was positive for catalase and oxidase. Growth occurred at 4-42 °C (optimum 30-37 °C), at pH 5. Read More

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Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance.

mSystems 2021 Jun 8:e0118520. Epub 2021 Jun 8.

School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom.

Staphylococcus aureus is a worldwide leading cause of numerous diseases ranging from food-poisoning to lethal infections. Methicillin-resistant S. aureus (MRSA) has been found capable of acquiring resistance to most antimicrobials. Read More

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Characterization of Campylobacter jejuni isolated from dogs and humans using flaA-SVR fragment sequencing in Ismailia, Egypt.

Comp Immunol Microbiol Infect Dis 2021 May 29;77:101675. Epub 2021 May 29.

Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ring road, Ismailia 41522, Egypt.

Introduction: Dogs are known as asymptomatic carriers forCampylobacter jejuni. The number of pet dogs is increasing in Egypt in the last decade.

Objective: This study aimed to investigate the frequency ofC. Read More

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gen. nov., sp. nov. (Chroococcales, Cyanobacteria), isolated from paddy fields in Iran.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra 3000-456, Portugal.

In Iran, polyphasic studies of unicellular cyanobacteria are still scarce, with more emphasis being placed on filamentous cyanobacteria in paddy fields and fresh water regions. In an effort to increase the knowledge of the diversity of unicellular cyanobacteria from paddy fields in Iran, we have isolated and characterized a new unicellular cyanobacterium strain. The strain was studied using a polyphasic approach based on morphological, ecological and phylogenetic analyses of the 16S-23S ITS rRNA gene region. Read More

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sp. nov. isolated from refrigerated dry-aged beef.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany.

A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2a with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains DSM 101070, DSM 108989, DSM 26521 and DSM 29166, placing it within the / branch of the genus . Additional based comparison revealed DSM 101070 as the nearest relative, with 98. Read More

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Genomic surveillance of in the Philippines, 2013-2014.

Western Pac Surveill Response J 2021 Jan-Mar;12(1):17-25. Epub 2021 Feb 26.

These authors contributed equally to this work.

Antimicrobial-resistant is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. We sequenced the whole genomes of 21 isolates collected in 2013-2014 by ARSP. Read More

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February 2021

Dynamics of Legionella Community Interactions in Response to Temperature and Disinfection Treatment: 7 Years of Investigation.

Microb Ecol 2021 Jun 5. Epub 2021 Jun 5.

Department of Biological, Geological, and Environmental Sciences, University of Bologna, via San Giacomo 12, 40126, Bologna, BO, Italy.

In man-made water distribution systems, Legionella community interactions remain unknown, due to their ability to change from sessile to planktonic states or live in viable but non-culturable forms, in response to anthropic and environmental stress. During 7 years of hospital Legionella surveillance, in 191 hot water positive samples, the interactions among the Legionella species, temperature, and disinfection treatment were evaluated. Legionella was isolated following ISO 11731:2017, and identification was performed by mip gene sequencing and sequence-based typing (SBT) for L. Read More

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Isolation and characterization of colistin-resistant Enterobacterales from chickens in Southeast Nigeria.

J Glob Antimicrob Resist 2021 Jun 3. Epub 2021 Jun 3.

Clinical Microbiology Laboratory, IRCCS Arcispedale S. Maria Nuova, AUSL Reggio Emilia, Italy. Electronic address:

Background: The resistance to colistin mediated by mobile elements had a broad impact worldwide. There is an intensified call for epidemiological surveillance of mcr in different reservoirs to preserve colistin for future generations. In Nigeria, the poultry industry is a key livestock sector. Read More

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Validation of MALDI-TOF for the early detection of the ST175 high-risk clone of Pseudomonas aeruginosa in clinical isolates belonging to a Spanish nationwide multicenter study.

Enferm Infecc Microbiol Clin (Engl Ed) 2021 Jun-Jul;39(6):279-282

Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain.

Introduction: Pseudomonas aeruginosa causes severe infections, particularly in healthcare settings and immunocompromised patients in whom MDR and XDR isolates are more prevalent. The aim of this study is to validate a method based on MALDI-TOF spectra analysis for early detection of the ST175 high-risk clone (HRC).

Methods: The MALDI-TOF spectra of the first 10 P. Read More

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February 2020

Helicobacter pylori in the Indonesian Malay's descendants might be imported from other ethnicities.

Gut Pathog 2021 Jun 4;13(1):36. Epub 2021 Jun 4.

Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama Machi, Yufu City, Oita, 879-5593, Japan.

Background: Even though the incidence of H. pylori infection among Malays in the Malay Peninsula is low, we observed a high H. pylori prevalence in Sumatra, which is the main residence of Indonesian Malays. Read More

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sp. nov. and sp. nov., isolated from a tidal flat.

Int J Syst Evol Microbiol 2021 Jun;71(6)

Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Republic of Korea.

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3 and YSTF-M6, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3 and YSTF-M6 belong to the genera and of the family , respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3 and the type strains of species and between strain YSTF-M6 and the type strains of species were 94. Read More

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Whole genome sequencing data used for surveillance of infections: detection of a large continuous outbreak, Denmark, 2019.

Euro Surveill 2021 Jun;26(22)

Statens Serum Institut, Department of Bacteria, Parasites and Fungi, Copenhagen, Denmark.

Background is one of the most frequent causes of bacterial gastroenteritis. outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical isolates was applied. Read More

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Molecular Epidemiology of Extensively-Drug Resistant Sequence Type 2 Co-Harboring and From Clinical Origin.

Infect Drug Resist 2021 25;14:1931-1939. Epub 2021 May 25.

Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan.

Background: The therapeutic management of carbapenem-resistant (CR-AB) represents a serious challenge to the public health sector because these pathogens are resistant to a wide range of antibiotics, resulting in limited treatment options. The present study was planned to investigate the clonal spread of CR-AB in a clinical setting.

Methodology: A total of 174 clinical isolates were collected from a tertiary care hospitals in Lahore, Pakistan. Read More

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Genetic diversity in a unique population of dugong (Dugong dugon) along the sea coasts of Thailand.

Sci Rep 2021 Jun 2;11(1):11624. Epub 2021 Jun 2.

Animal Bone and Joint Research Laboratory, Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.

Dugong (Dugong dugon) populations have been shrinking globally, due in large part to habitat fragmentation, degradation and ocean pollution, and today are listed as Vulnerable by the IUCN. Thus, determining genetic diversity in the remaining populations is essential for conservation planning and protection. In this study, measures of inter-simple sequence repeat (ISSR) markers and mtDNA D-loop typing were used to evaluate the genetic diversity of 118 dugongs from skin samples of deceased dugongs collected in Thai waters over a 29-year period. Read More

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Distribution of fluoroquinolone resistance determinants in Carbapenem-resistant Klebsiella pneumoniae clinical isolates associated with bloodstream infections in China.

BMC Microbiol 2021 Jun 2;21(1):164. Epub 2021 Jun 2.

Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200082, P. R. China.

Background: The rate of fluoroquinolone (FQ) resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) is high. The present study aimed to investigate the distribution of fluoroquinolone resistance determinants in clinical CRKP isolates associated with bloodstream infections (BSIs).

Results: A total of 149 BSI-associated clinical CRKP isolates collected from 11 Chinese teaching hospitals from 2015 to 2018 were investigated for the prevalence of fluoroquinolone resistance determinants, including plasmid-mediated quinolone resistance (PMQR) genes and spontaneous mutations in the quinolone resistance-determining regions (QRDRs) of the gyrA and parC genes. Read More

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Genetic diversity of healthcare-associated methicillin-resistant Staphylococcus aureus isolates from Southern Iran.

Acta Microbiol Immunol Hung 2021 Jun 2. Epub 2021 Jun 2.

1Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.

Staphylococcus aureus is a common pathogen causing hospital infections. The increasing rate of healthcare-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) in developing countries has led to many public health problems. This study aimed to investigate the molecular epidemiology as well as the antibiotic resistance pattern of clinical isolates of MRSA from Southern Iran. Read More

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Genomic Characterization of the Novel sp. Isolated from the Blood of a (Pallas, 1811).

Vector Borne Zoonotic Dis 2021 Jun 16;21(6):432-440. Epub 2020 Jun 16.

UMR VITROME, Aix-Marseille University, Institut pour la Recherche et le Développement, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.

species are reemerging infectious agents that are transmitted by arthropod vectors among animals and/or humans. At least 13 of the 35 currently recognized species are pathogenic for humans. Most of the pathogenic species, except and are zoonotic agents with animal reservoirs, including cats, dogs, coyotes, foxes, cattle, and rodents. Read More

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Genomic analysis and phylogenetic position of the complex IncC plasmid found in the Spanish monophasic clone of Salmonella enterica serovar Typhimurium.

Sci Rep 2021 Jun 1;11(1):11482. Epub 2021 Jun 1.

Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006, Oviedo, Spain.

pUO-STmRV1 is an IncC plasmid discovered in the Spanish clone of the emergent monophasic variant of Salmonella enterica serovar Typhimurium, which has probably contributed to its epidemiological success. The sequence of the entire plasmid determined herein revealed a largely degenerated backbone with accessory DNA incorporated at four different locations. The acquired DNA constitutes more than two-thirds of the pUO-STmRV1 genome and originates from plasmids of different incompatibility groups, including IncF (such as R100 and pSLT, the virulence plasmid specific of S. Read More

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Presence of plasmid-mediated quinolone resistance (PMQR) genes in non-typhoidal Salmonella strains with reduced susceptibility to fluoroquinolones isolated from human salmonellosis in Gyeonggi-do, South Korea from 2016 to 2019.

Gut Pathog 2021 Jun 1;13(1):35. Epub 2021 Jun 1.

Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, South Korea.

Non-typhoidal salmonellosis remains a pressing public health problem worldwide. Quinolones, particularly fluoroquinolones, are widely used to treat various infections, including non-typhoidal salmonellosis, which can be a serious illness. The emergence of fluoroquinolone-resistant Salmonella has resulted in treatment failure and high mortality rates. Read More

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